Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
By onDopamine (DA) neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of DA neurons is embedded within complex brain tissues, making it difficult to access the DA neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of DA neurons. Our dataset reveals the proteomic architecture underlying axonal transport, dopamine transmission, and axonal metabolism in DA neurons. We find a significant enrichment of proteins encoded by Parkinson’s disease-linked genes in dopaminergic axons, including proteins with previously undescribed axonal localization. Our proteomic datasets comprise a significant resource for axonal and DA neuronal cell biology, while the methodology developed here will enable future studies of other neural cell types. This mass spectrometry proteomics dataset is a part of "Subcellular proteomics of dopamine neurons in the mouse brain" (Hobson et. al, 2022)
Structure of human ULK1 complex core (2:1:1 stoichiometry)
By onStructure of human ULK1 complex core (2:1:1 stoichiometry)
Structure of PPM1H phosphatase with manganese ions at the active site
By onStructure of PPM1H phosphatase with manganese ions at the active site (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7N0Z.
Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
By onStructure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture (Method: ELECTRON MICROSCOPY, Resolution: 5.85 Å, Aggregation State: PARTICLE, Reconstruction Method: SINGLE PARTICLE).
Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
By onStructure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
Primary data associated with doi: 10.1101/2022.04.25.489459 (A Feed-forward Pathway Drives LRRK2 kinase Membrane Recruitment and Apparent Activation)
By onRaw immunoblotting data; tabular data for quantifications; immunofluorescence images.
Structure of human ULK1C:PI3KC3-C1 supercomplex
By onStructure of human ULK1C:PI3KC3-C1 supercomplex
Differential response of α-synuclein expression to bacterial ligands and metabolites in mouse enteroendocrine cells
By onDataset for manuscript " α-synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells". Tabs in excel file are title with the figure number.
Primary data associated with the manuscript “Genome-wide screen reveals Rab12 GTPase as 2 a critical activator of Parkinson’s disease-linked LRRK2 kinase” (3/3)
By onPrimary data associated with the manuscript, "Genome-wide screen reveals Rab12 GTPase as 2 a critical activator of Parkinson’s disease-linked LRRK2 kinase."
Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer
By onCrystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer (Method: X-RAY DIFFRACTION Resolution: 2.41 Å R-Value Free: 0.251 R-Value Work: 0.204 R-Value Observed: 0.205)
Primary data associated with the manuscript “Whole proteome copy number dataset in primary mouse cortical neurons” (doi: 10.1016/j.dib.2023.109336)
By onRaw data reported in Supplementary table in "Whole Proteome Copy Number Dataset in Primary Mouse Cortical Neurons."
Primary data associated with the manuscript “CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data” (doi: https://doi.org/10.1101/2023.07.25.550405)
By onRaw immunoblotting data and their quantitation and graphs obtained using GraphPad Prism; PCR and sequencing data confirming that PPM1H-BromoTag clone E5 (used for all experiments in the manuscript) is a homozygous clone.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Cell Surface FCS
By onFCS files corresponding to the cell surface experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"
shoebridges/asap_phosphosites: Preview Release
By onSource data associate with publication "Unconventional Initiation of PINK1/Parkin Mitophagy by Optineurin"
Structural basis for the specificity of PPM1H phosphatase for Rab GTPases
By onRaw data associated with DOI: 10.15252/embr.202152675
Mass spectrometry proteomic data supporting the PPM1H/Rab8A crosslinking study described in doi: 10.15252/embr.202152675
By onRaw data associated with DOI: 10.15252/embr.202152675
Primary data associated with doi: 10.1042/BCJ20220308 (PKC isoforms activate LRRK1 kinase by phosphorylating conserved residues (Ser1064, Ser1074 and Thr1075) within the CORB GTPase domain)
By onRaw immunoblotting data; immunofluorescence microscopy images; tabular data for quantification; autoradiograph films; scans of Coomassie-stained protein gels; Prism files with statistical analysis.
Phosphosite mapping on PI3Kc1 by ULK1 and TBK1 kinases.
By onPhosphosite mapping on PI3Kc1 by ULK1 and TBK1 kinases.
Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation data
By onAtomistic molecular dynamics simulation data set accompanying manuscript "Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore".
